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PTM Flashcards

1
Q

what do cells need to do to maintain homeostasis

A

to detect changes in their environment and respond accordingly

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2
Q

how quick are the response to homeostatic changes

A

~ms

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3
Q

what can dynamic-rapid responses not be achieved using

A

gene transcriptional regulation

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4
Q

what are PTMs suitable for

A

relaying rapid messages within the cell as they are dynamic, quick and reversible

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5
Q

are PTMs reversible

A

yes

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6
Q

what is the definition of PTM

A

post-translational modification (the modifications proteins undergo after translation)

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7
Q

what are PTMs and what are they introduced to

A

covalent additions to amino acids

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8
Q

what do PTMs do to the modified residue

A

change the physicochemical properties

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9
Q

what are examples of small group PTMs

A

phosphate or acetyls

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10
Q

what are examples of large polypeptide PTMs

A

Ubiquitin or SUMO

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11
Q

how many PTMs have been identified

A

over 200

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12
Q

what are some PTM examples

A

phosphorylation, acetylation, ubiquitination, SUMOylation and methylation

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13
Q

what are the writers and erasers of phosphorylation

A

kinase and phosphatase

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14
Q

what are the writers and erasers of ubiquitination

A

ubiquitin E3 ligase and deubiquitinase

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15
Q

what are the writers and erasers of SUMOylation

A

SUMO E3 ligase and deSUMOylase

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16
Q

what are the writers and erasers of acetylation

A

acetyltransferase and deacetylase

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17
Q

what are the writers and erasers of methylation

A

methyltransferases and demethylases

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18
Q

how many kinds of kinase are there

A

more than 500

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19
Q

how many kinds of phosphatases are there

A

200

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20
Q

how do kinases work

A

bind to an ATP molecule and takes up the gamma phosphate, gamma then can bind to the substrate

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21
Q

what are the characteristics of phosphate groups

A
  • large and bulky
  • have a specific “shape”
  • negatively charged (up to 2 negative charges) at a neutral pH
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22
Q

what happens when you add a phosphate group to a protein

A

it alters the shape and charge of the protein

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23
Q

what can PTMs induce

A

conformational changes and promote interaction with proteins that have affinity for modified residues

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24
Q

what are the 2 types of conformational change

A
  • long-range disruption
  • long-range ordering
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25
what can PTMs modulate
- activity (either promote or inhibit) - localisation - stability - complex formation - selectivity
26
what is an example of PTMs modulating activity
kinase activity by phosphorylation of its activation loop
27
what is an example of PTMs modulating localisation
by modifying/masking Nuclear Localisation SIgnals
28
what is an example of PTMs modulating stability
ubiquitin-mediated proteasomal degradation
29
what is an example of PTMs modulating complex formation
the formation of docking sites
30
what is an example of PTMs modulating selectivity
promoter specificity mediated by phosphorylation (eg p53)
31
can a protein be modified by multiple PTMs
yes, they can be modified by more than one type of PTM OR modified by the same PTM at different residues
32
what happens when PTMs are seperated in time
they can occur sequentially on a single site in a protein
33
what happens in positive crosstalk
one PTM serves as a signal for the addition or removal of a second PTM
34
what happens in negative crosstalk
it can be a direct competition for modification of a single residue in a protein, or indirectly by masking the recognition site for a second PTM
35
how can you measure PTMs in cells
- antibodies that recognise specific PTMs - mass spectrometry (measures the mass-to-charge ratio of one or more molecules present in a sample)
36
how are modified-specific antibodies generated
using a modified peptide as an antigen
37
how do modified-specific antibodies work
antibody recognises both the modified group AND parts of the peptide surrounding the modified site
38
what are modified-specific antibodies usually used for analysiing
phosphorylation, acetylation and methylation
39
what are the advantages of modified-specific antibodies
- cheap - can provide quantitative information - can identify subtle differences - very sensitive - highly specific
40
what are the disadvantages of modified-specific antibodies
- only works if you already have information about where your protein is modified and the type of modification - there are not antibodies avaliable for each modified protein - producing new antibodies is time consuming, expensive and not always successful
41
what is mass specotrometry
an analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio. these spectra are used to elucidate the chemical structures, such as peptides and other chemical compounds
42
what is the order of a mass spectrometry reading
sample - gass/liquid chromatography (seperation step) - ionisation interface - mass spectrometer (measures mass)
43
what do peaks in a mass spectrometer reading show
that phosphorylation has occured
44
what can mass spectrometers not read
they cannot determine between AA numbers - if there are 2 serines next to each other it cant determine which is which
45
what are the advantages of mass spectrometry
- provides unbiased/untargeted information - it can differentiate very similar proteins/isoforms (ie substitution in a single AA) - it can generate a huge amount of information (eg it can identify different modifications in hundreds of proteins in the same sample) - it can be quantitative (allows to make clear differentiations between 2 species (eg KO and WT))
46
what are the disadvantages of mass spectrometry
- can be expensive and time consuming - often difficult to pinpoint the position of the phosphorylation site with single AA residues - very abundant proteins will mask low abundance proteins (eg if hair falls in, all that it will show is keratin) - you need the expertise
47
what are protein kinases
enzymes that catalyse the transfer of phosphate from ATP to their substrate
48
are kinases specific
yes
49
are phosphatases specific
no, they are "promiscious"
50
how many genes code for kinases in the human genome
538 (2% of total genes)
51
which human kinases are most abundant
ser/Thr or Tyr kinases
52
what can kinases be clustered into
groups, families and sub-families of increasing sequence similarity and biochemical function
53
what is the structure of protein kinases
all have a conserved core with the same basic 3D organisation, comprising of 2 lobes with the active site, where the ATP binds, in a cleft between the lobes
54
what do tyrosine kinase signalling pathways control
the most fundamental processes of the cell (such as cell proliferation, differentiation, motility and cell death / survival)
55
what happens to tyrosine kinases in tumour cells
they are often deregulated due to hyper-activating mutations, amplification/overexpression or loss of negative regulation
56
what do aberrant constitutive phosphorylation sustain
oncogenic signal transduction pathways
57
how many of known oncogenes are protein kinases
approx half
58
how many oncology drugs that target kinases have been approved
around 40
59
what is the major difference between non-covalent and covalent inhibitors
non-covalent inhibitors are reversible whereas covalent inhibitors are irreversible
60
what are the characteristics of type I protein kinase inhibitors
- reversible - binds to ATP site - is ATP-competitive - low selectivity
61
what are the characteristics of type II protein kinase inhibitors
- reversible - binds to ATP site and DFG pocket - not ATP-competitive - high selectivity
62
what are the characteristics of type III protein kinase inhibitors
- reversible - allosteric binding (outside of ATP-binding site) - not ATP-competitive - very high selectivity
63
what are the characteristics of type IV protein kinase inhibitors
- reversible - allosteric binding (substrate binding domain) - not ATP-competitive - very high selectivity
64
what are the characteristics of covalent inhibitors
- irreversible - binds to ATP site - not ATP-competitive - low selectivity

cell proliferation (12 decks)

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